Fungal, Bacterial, and Archaeal Diversity in Soils Beneath Native and Introduced Plants in Fiji, South Pacific

Abstract

The Fiji Islands is an archipelago of more than 330 islands located in the tropics of the South Pacific Ocean. Microbial diversity and biogeography in this region is still not understood. Here, we present the first molecular characterization of fungal, bacterial, and archaeal communities in soils from different habitats within the largest Fijian island, Viti Levu. Soil samples were collected from under native vegetation in maritime-, forest-, stream-, grassland-, and casuarina-dominated habitats, as well as from under the introduced agricultural crops sugarcane, cassava, pine, and mahogany. Soil microbial diversity was analyzed through MiSeq amplicon sequencing of 16S (for prokaryotes), ITS, LSU ribosomal DNA (for fungi). Prokaryotic communities were dominated by Proteobacteria (~ 25%), Acidobacteria (~ 19%), and Actinobacteria (~ 17%), and there were no indicator species associated with particular habitats. ITS and LSU were congruent in β-diversity patterns of fungi, and fungal communities were dominated by Ascomycota (~ 57–64%), followed by Basidiomycota (~ 20–23%) and Mucoromycota (~ 10%) according to ITS, or Chytridiomycota (~ 9%) according to LSU. Indicator species analysis of fungi found statistical associations of Cenococcum, Wilcoxina, and Rhizopogon to Pinus caribaea. We hypothesize these obligate biotrophic fungi were co-introduced with their host plant. Entoloma was statistically associated with grassland soils, and Fusarium and Lecythophora with soils under cassava. Observed richness varied from 65 (casuarina) to 404 OTUs (cassava) for fungi according to ITS region, and from 1268 (pine) to 2931 OTUs (cassava) for bacteria and archaea. A major finding of this research is that nearly 25% of the fungal OTUs are poorly classified, indicative of novel biodiversity in this region. This preliminary survey provides important baseline data on fungal, bacterial, and archaeal diversity and biogeography in the Fiji Islands.

Notes

Acknowledgements

We are grateful to the Fijian land-owning clans of the Vanua Davutukia, Korolevu-i-wai who allowed us access to their land to collect samples. We thank Jon Dahl from the Soil and Plant Nutrient Laboratory at Michigan State University for assistance.

Author Contribution

G. B. and V. B. designed the research, sampled the soils in Fiji, and wrote the manuscript. G. M. N. B. extracted DNA, prepared the Illumina library, analyzed the data, and wrote the manuscript. All authors approved the final version for submission.

Funding Information

GMNB and GB acknowledge support from Michigan State University AgBioResearch NIFA project MICL02416 and National Science Foundation (NSF) DEB1737898.

Supplementary material

Figure S1Bar plots of relative abundance, based on ITS, LSU and 16S rDNA genes, at ordinal-level. For 16S only the first 50 taxa are shown. Habitats dominated by introduced plant hosts are denoted in bold. (PDF 68 kb)

Figure S2Shepard diagrams for ITS, LSU and 16S NMDS graphs reported in Fig. 3. The plot shows of ordination distances against original dissimilarities. Non-metric fit is based on stress value of the NMDS ordination and calculated as R2 = 1-S*S. Linear fit is the squared correlation between fitted values and ordination distances. (PDF 234 kb)

Figure S4Boxplot of distance to centroids of every sampling location (i.e., site) for ITS, LSU and 16S rDNA. A p value from ANOVA of the distances to group centroids is also reported (perm. = 9999), to test if one or more sample group at each site is more variable than the others. Sites dominated by introduced plant hosts are denoted in bold. (PDF 29.3 kb)

Table S1List of the first 10 top abundant fungal OTUs detected in each of the 18 sites sampled. Taxonomy assignment using RDP classifiers against the UNITE database, taxonomy assignment using BLAST against GenBank database (https://www.ncbi.nlm.nih.gov/genbank/), max score, total score, query coverage, % sequence identity, e-value and sequence reference ID of the best match are reported. (XLSX 14.5 kb)